All cells after denoising
Major cell types
Only major cell types
prcnt_by_pt <- ClassAbundanceByPt(data=annot_df, ptID_col = 'pt_ID',
class_col = 'cell_type')
rownames(prcnt_by_pt) <- paste0(rownames(prcnt_by_pt), '_', ref$CANARY)
levels(annot_df$cell_type)
## [1] "Endothelial" "Epithelial" "Immune" "Mesenchymal"
# Dendrograms and barplots
dendrogram_barplot(prcnt_by_pt, dist_method = 'euclidean', hclust_method = 'ward.D')


dendrogram_barplot(prcnt_by_pt, dist_method = 'euclidean', hclust_method = 'complete')


# Correlation plot
corr_plot(prcnt_by_pt)

ggpubr::ggscatter(prcnt_by_pt, x = "Endothelial", y = 'Immune',
add = "reg.line", conf.int = TRUE, combine = TRUE,
cor.coef = TRUE, cor.method = "spearman", add.params = list(color = 'gray'),
xlab = "Endothelial cells", ylab = 'Immune cells')
## `geom_smooth()` using formula 'y ~ x'

# Differential abundance
x <- DA_analysis(annot_df, ref, class_col='cell_type', group_levels=c('G','P'),
group_col = 'CANARY', ptID_col = 'pt_ID')
##
## Attaching package: 'operators'
## The following objects are masked from 'package:base':
##
## options, strrep
##
## Attaching package: 'dplyr'
## The following object is masked from 'package:operators':
##
## %>%
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
x$pvals
## cell_type p.value FDR_corrected
## 1 Endothelial 0.1714286 0.6349206
## 2 Epithelial 0.9142857 0.9142857
## 3 Immune 0.3523810 0.6349206
## 4 Mesenchymal 0.4761905 0.6349206
Differential protein expression
med_endo <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
celltype_name='Endothelial', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
med_epi <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
celltype_name='Epithelial', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_fibmes <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
celltype_name='Mesenchymal', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_imm <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='cell_type',
celltype_name='Immune', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_tcells <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype2',
celltype_name='T_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_CD8T <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
celltype_name='Tc_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
med_CD4T <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
celltype_name='Th_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_mye <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
celltype_name='Myeloid', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
med_NK <- median_by_pt(annot_df, ref, subset_celltype=T, celltype_col='subtype',
celltype_name='NK_cells', ask_features=F, ft_idxs = c(15, 17:31, 33:35, 37:48, 50, 51),
ptID_col = 'pt_ID', groups=c('G', 'P'))
## Warning in wilcox.test.default(exp_median[ig1, i], exp_median[ig2, i]): cannot
## compute exact p-value with ties
Endothelial cells
## Using CANARY, pt_ID as id variables

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.1714286 0.7619048
## 2 145Nd_CD31 0.4761905 0.7619048
## 3 146Nd_Thioredoxin 0.3523810 0.7619048
## 4 147Sm_b-CAT 0.4761905 0.7619048
## 5 156Gd_Vimentin 1.0000000 1.0000000
## 6 158Gd_p-STAT3 0.7619048 0.8465608
## 7 160Gd_MDM2 0.6095238 0.7619048
## 8 161Dy_Cytokeratin 0.4761905 0.7619048
## 9 163Dy_TP63 0.6095238 0.7619048
## 10 174Yb_HLA-DR 0.1714286 0.7619048
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
Fibroblasts/Mesenchymal cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(0, 0.0958118253303701, 0.284162729407862, :
## cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.802649816095183, 0.215492384630114,
## 0.0605647943338007, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.76190476 0.9142857
## 2 142Nd_ccasp3 0.91428571 0.9142857
## 3 155Gd_CD56 0.47619048 0.8571429
## 4 156Gd_Vimentin 0.91428571 0.9142857
## 5 158Gd_p-STAT3 0.11428571 0.5142857
## 6 160Gd_MDM2 0.19945761 0.5983728
## 7 163Dy_TP63 0.47619048 0.8571429
## 8 170Yb_CD3 0.91406196 0.9142857
## 9 174Yb_HLA-DR 0.03809524 0.3428571
## Warning in wilcox.test.default(c(0, 0.0958118253303701, 0.284162729407862, :
## cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.802649816095183, 0.215492384630114,
## 0.0605647943338007, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
Immune cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.06708656196431, 0.066910551904235,
## 3.04431780411568, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.202586121632867, 0.0645635010399363, : cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(c(0.501727573634015, 0.130067040154415,
## 0.712432219756351, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.1055017 0.8571429
## 2 154Sm_CD45 0.4761905 0.9523810
## 3 156Gd_Vimentin 0.4761905 0.9523810
## 4 158Gd_p-STAT3 0.7619048 0.9523810
## 5 159Tb_CD4 0.9140620 1.0000000
## 6 163Dy_TP63 0.6095238 0.9523810
## 7 166Er_CD44 1.0000000 1.0000000
## 8 170Yb_CD3 0.7619048 0.9523810
## 9 171Yb_CD11b 0.3314247 0.9523810
## 10 174Yb_HLA-DR 0.1714286 0.8571429
## Warning: Removed 1 rows containing non-finite values (stat_boxplot).
## Warning: Removed 1 rows containing non-finite values (stat_signif).
## Warning in wilcox.test.default(c(3.06708656196431, 0.066910551904235,
## 3.04431780411568, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.202586121632867, 0.0645635010399363, : cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(c(0.501727573634015, 0.130067040154415,
## 0.712432219756351, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[10L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
T cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.08923421925895, 0.0448292529698694,
## 2.91669547906524, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.15951925690942, 0.142600017626425,
## 1.11836487985089, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.06656797 0.5325437
## 2 154Sm_CD45 0.25714286 0.6349206
## 3 156Gd_Vimentin 0.47619048 0.6349206
## 4 159Tb_CD4 0.74838121 0.8552928
## 5 163Dy_TP63 0.91428571 0.9142857
## 6 166Er_CD44 0.25714286 0.6349206
## 7 170Yb_CD3 0.35238095 0.6349206
## 8 174Yb_HLA-DR 0.47619048 0.6349206
## Warning in wilcox.test.default(c(3.08923421925895, 0.0448292529698694,
## 2.91669547906524, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.15951925690942, 0.142600017626425,
## 1.11836487985089, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
CD8 T cells
## Using CANARY, pt_ID as id variables

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.03174603 0.2539683
## 2 154Sm_CD45 0.90476190 0.9047619
## 3 156Gd_Vimentin 0.55555556 0.8344671
## 4 163Dy_TP63 0.19047619 0.5079365
## 5 166Er_CD44 0.73015873 0.8344671
## 6 168Er_CD8 0.55555556 0.8344671
## 7 170Yb_CD3 0.73015873 0.8344671
## 8 174Yb_HLA-DR 0.11111111 0.4444444
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[8L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
CD4 T cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(0, 0.0561621657336121, 0, 0), c(0, 0,
## 1.50456532271426, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.6095238 0.9142857
## 2 154Sm_CD45 0.3523810 0.7928571
## 3 156Gd_Vimentin 0.2571429 0.7714286
## 4 159Tb_CD4 0.6095238 0.9142857
## 5 163Dy_TP63 0.7619048 0.9795918
## 6 166Er_CD44 0.1714286 0.7714286
## 7 169Tm_CD24 1.0000000 1.0000000
## 8 170Yb_CD3 0.2571429 0.7714286
## 9 174Yb_HLA-DR 0.9142857 1.0000000
## Warning in wilcox.test.default(c(0, 0.0561621657336121, 0, 0), c(0, 0,
## 1.50456532271426, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[9L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
Myeloid cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(3.30075534359615, 0.0972935332589382,
## 3.31354462816258, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.62386202915046, 0.717296683223608,
## 2.44717234480325, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.748820669157824, 0.123253874437529,
## 1.67192224879611, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.63662474810693, 0.0913139040611759,
## 1.20841095112529, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 144Nd_HLA-ABC 0.1645218 0.9523810
## 2 145Nd_CD31 0.4541743 0.9523810
## 3 146Nd_Thioredoxin 0.5929097 0.9846154
## 4 154Sm_CD45 0.4761905 0.9523810
## 5 156Gd_Vimentin 0.4761905 0.9523810
## 6 158Gd_p-STAT3 0.3523810 0.9523810
## 7 159Tb_CD4 0.7461278 0.9846154
## 8 160Gd_MDM2 0.9142857 0.9846154
## 9 163Dy_TP63 1.0000000 1.0000000
## 10 166Er_CD44 0.9142857 0.9846154
## 11 171Yb_CD11b 0.4761905 0.9523810
## 12 172Yb_p-S6 0.9142857 0.9846154
## 13 174Yb_HLA-DR 0.2571429 0.9523810
## 14 175Lu_PD-L1 0.7619048 0.9846154
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
## Warning: Removed 4 rows containing non-finite values (stat_signif).
## Warning in wilcox.test.default(c(3.30075534359615, 0.0972935332589382,
## 3.31354462816258, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.62386202915046, 0.717296683223608,
## 2.44717234480325, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.748820669157824, 0.123253874437529,
## 1.67192224879611, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(0.63662474810693, 0.0913139040611759,
## 1.20841095112529, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
NK cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(1.64257353775631, 0.200933284463877,
## 1.65031204702996, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 142Nd_ccasp3 0.60952381 0.7757576
## 2 144Nd_HLA-ABC 0.11428571 0.3428571
## 3 145Nd_CD31 0.17142857 0.3428571
## 4 146Nd_Thioredoxin 0.16452182 0.3428571
## 5 148Nd_HER2 0.17142857 0.3428571
## 6 154Sm_CD45 0.47619048 0.6666667
## 7 155Gd_CD56 1.00000000 1.0000000
## 8 156Gd_Vimentin 0.17142857 0.3428571
## 9 158Gd_p-STAT3 0.91428571 0.9846154
## 10 160Gd_MDM2 0.47619048 0.6666667
## 11 163Dy_TP63 0.03809524 0.2666667
## 12 166Er_CD44 0.76190476 0.8888889
## 13 172Yb_p-S6 0.25714286 0.4500000
## 14 174Yb_HLA-DR 0.03809524 0.2666667
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
## Warning: Removed 4 rows containing non-finite values (stat_signif).
## Warning in wilcox.test.default(c(1.64257353775631, 0.200933284463877,
## 1.65031204702996, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[14L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
Epithelial cells
## Using CANARY, pt_ID as id variables
## Warning in wilcox.test.default(c(2.33079293987923, 0.0582644008491126,
## 1.75087785796523, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.63156525887895, 0.322305842850225,
## 1.32203451663395, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.13653172069154, 0.0527562183492093,
## 1.50292979733778, : cannot compute exact p-value with ties

## Protein p.value FDR_corrected
## 1 141Pr_EpCAM 0.11428571 0.4114286
## 2 142Nd_ccasp3 0.35238095 0.5714286
## 3 144Nd_HLA-ABC 0.16452182 0.4408163
## 4 147Sm_b-CAT 0.17142857 0.4408163
## 5 148Nd_HER2 0.03809524 0.4114286
## 6 151Eu_TTF1 0.09898793 0.4114286
## 7 154Sm_CD45 0.47619048 0.5714286
## 8 155Gd_CD56 0.76190476 0.8067227
## 9 156Gd_Vimentin 0.47619048 0.5714286
## 10 158Gd_p-STAT3 0.35238095 0.5714286
## 11 160Gd_MDM2 0.91428571 0.9142857
## 12 161Dy_Cytokeratin 0.11428571 0.4114286
## 13 162Dy_MET 0.25714286 0.5142857
## 14 163Dy_TP63 0.47619048 0.5714286
## 15 164Dy_CK7 0.47619048 0.5714286
## 16 165Ho_EGFR 0.10550173 0.4114286
## 17 170Yb_CD3 0.60952381 0.6857143
## 18 174Yb_HLA-DR 0.25714286 0.5142857
## Warning in wilcox.test.default(c(2.33079293987923, 0.0582644008491126,
## 1.75087785796523, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.63156525887895, 0.322305842850225,
## 1.32203451663395, : cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(1.13653172069154, 0.0527562183492093,
## 1.50292979733778, : cannot compute exact p-value with ties
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[18L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomSignif() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues